Johan Enell wrote: > I think it's best to discuss this in a new thread. > > The easiest way to go around this bug is to define a directory for the > Experiment. Edit Experiment and add a directory.
Ok, thanks. That got me a bit further... > > You will also need to change the field '_allIntensities' to > intesity1\tintensity2. The suport for allIntensities till be added in a > future release. > So I changed this to intensity1 (only), since I was trying to analyse some single channel data (I haven't loaded any 2 channel data in BASE2 yet). I then had to change the base 1.2 file export uniqueName molbio.mgh.harvard.edu/dpark/limitint to 'basefile-general.pl' and the exec path to /usr/local/base2/www/plugins/molbio.mgh.harvard.edu/dpark/. I guess execName is sensibly ignored...I created the directory to run the plugin within the experiment. I then run it and get: 'Error: Can't find the columns intensity1/intensity2 or l2ratio1_2/l10intgmean1_2. No data could be inmported.' Maybe I am expecting too much until allIntensities is working.... I will load in some 2 channel data and do some further testing. How do I reopen a ticket if I need to ? >>I have a few follow up questions and comments about plugins...I am trying to >>get MGH plugins from BASE2 working. Unfortunately I am not having much luck >>(see ticket http://base.thep.lu.se/ticket/511). >> >> > It is fixed > >>So my questions are: >> >>1) Which plugins have been successfully tested in Base1PluginExecuter (just >>so I can rule out it's not me!)? >> >> > I've successfully with MergeBioassays, > http://lev.thep.lu.se/trac/baseplugins/wiki/onk.lu.se.MergBioAssay > >>2) Do you require some help testing Base1PluginExecuter? I am happy to help >>here to get this working for the common good and also I have a several custom >>plugins I have written in R and perl (and other plugins used in BASE 1.2) >>that I would really like to use on the data in BASE. Also I can't really move >>all my users of BASE 1.2 across to BASE2 until I get these working, since >>they use these as part of their daily analysis. >> >> > Yes, we appreciate all help that we can get. Especially testing since it > feels like we never have time to do it as thorough as we would like. As > far as I know all base 1 plugins should work except for those using the > option 'geneAverages'. > >>3) What are the plans to support non-Java plugins (via development of >>Base1PluginExecuter or otherwise) given that R and perl are very popular >>languages in bioinformatics and for arrays most serious >>analysis is done using R? >> >> > I leave this question open for now. Let me come back on this. > Just my 2c. If all the BASE1.2 plugins can be got to work robustly then perhaps you can evolve the BASE 1.2 plugin executer code? With an extra configuration screen for passing in variables this would be useful...Also long term it could be worth looking at what the EBI are doing with the developer API for the Expression Profiler (http://www.ebi.ac.uk/expressionprofiler/). The bonus if this approach was implemented would mean any plugins for BASE could in theory work in Expression Profiler too. I realise the latter would take a fair amount of work and coordination...:-) BTW where is the central list of BASE 1.2 plugins listed these days? If it is verified they work in BASE 2 it would be good to check them into the subversion repository, with the appropriate config files. Regards and thanks, Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
